LAMMPS Non-Features

LAMMPS is designed to be a fast, parallel engine for molecular dynamics (MD) simulations. As such, LAMMPS itself provides only a modest amount of functionality for setting up simulations and analyzing their output.

Specifically, LAMMPS itself does not:

• run thru a GUI
• build molecular systems
• assign force-field coefficients automagically
• perform sophisticated analyses of your MD simulation
• visualize your MD simulation
• plot your output data

Here are suggestions as to how you can perform these tasks.

• GUI: LAMMPS can be built as a library and a Python wrapper that wraps the library interface is provided. Thus, GUI interfaces can be written in Python (or C or C++ if desired) that run LAMMPS and visualize or plot its output. Examples of this are provided in the python directory and described in Section python of the manual.
• Builder: Several pre-processing tools are packaged with LAMMPS. Some of them convert input files in formats produced by other MD codes such as CHARMM, AMBER, or Insight into LAMMPS input formats. Some of them are simple programs that will build simple molecular systems, such as linear bead-spring polymer chains. The moltemplate program is a true molecular builder that will generate complex molecular models. See the tools directory and Section tools of the manual for a discussion of the various tools. The Molecular Builder page of the WWW site describes moltemplate and the VMD topotools program.
• Force-field assignment: The conversion tools described in the previous bullet for CHARMM, AMBER, and Insight will also assign force field coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER, or Accelerys force field files.
• Simulation analyses: If you want to perform analyses on-the-fly as your simulation runs, see the computes and fixes LAMMPS provides, which can be used in an input script. It is also possible to write your own compute or fix to add to LAMMPS. For post-processing, LAMMPS output such as dump files can be converted into formats used by other MD or post-analysis codes. Scripts provided with the python tool in the tools directory will extract and massage data in dump files to make it easier to import into other programs. See the tools directory and Section tools of the manual for a discussion of the various tools.
• Visualization: A very simple (but fast) viz tool called xmovie is provided with LAMMPS, described in Section tools of the LAMMPS manual. See the Other Codes page of the WWW site for visualization packages that can be used with LAMMPS output data.
• Plotting: See the next bullet about Pizza.py as well as Section python of the manual for examples of plotting LAMMPS output. Scripts provided with the python tool in the tools directory will extract and massage data in log and dump files to make it easier to analyze and plot. See the tools directory and Section tools of the manual for a discussion of the various tools.
• Pizza.py: Our group has also written a separate toolkit called Pizza.py which provides tools for doing setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS simulations. It thus provides some functionality for several of the above bullets. Pizza.py is written in Python and is available for download from this page.

Features that LAMMPS does not currently have, but which are planned for future releases, are discussed in this section of the LAMMPS documentation.